MTI-R01_0110/README.md

# Marmoset Tracer-Injection [R01_0110]

Authors: Akiya Watakabe<sup>1</sup>*, Henrik Skibbe<sup>2</sup>

1. Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science
2. Brain Image Analysis Unit, RIKEN Center for Brain Science

*corresponding authors: Akiya Watakabe (akiya.watakabe@riken.jp)


## DATASET DESCRIPTION
    
This dataset contains **TissueCyte** images produced during **tracer injection** experiment on Marmoset **R01_0110**

* Microscopy images and annotations: Akiya Watakabe.
* Image post-processing: Henrik Skibbe.


For more details see https://dataportal.brainminds.jp/marmoset-tracer-injection


## EXPERIMENT METADATA
|||
|----|-----|
|Brain/MINDS ID|R01_0110|
|Group|Yamamori|
|Lab identifier|TT77|
|Region of injection|A45|
|Side of injection|left|
|Summary|A45 injection.  Small spread in A47L.  Weak tracer signals.  Projections to visual areas may suggest its position as FEF for small saccade.   |
|Known issues|Expression is low.  In particular, low expession in layer 6.   Potential interference of AAV-smFP constructs.|
|Age|6.7|
|Sex|F|
|Body weight (g)|386|
|Date of birth|20120719|
|Injection date|20190219|
|Survival period (day)|27|
|&#x00A0;Tracer **1** |(thy1-tTA 1/TRE-clover 1/TRE-Vamp2mPFC 0.25)x10e12 vg/ml|
|&#x00A0;Direction|anterograde|
|&#x00A0;Method|0.2ul x 1 (@ 1.8 mm) 5min |
|&#x00A0;Tracer **2** |AAV2retro-EF1-cre: 1.5x10e12 vg/ml|
|&#x00A0;Injection Site|Coinjection with tracer 1|
|&#x00A0;Direction|retro|
|&#x00A0;Tracer **3** |10 % BDA|
|&#x00A0;Injection Site|contra/MT|
|&#x00A0;Direction|antero|
|&#x00A0;Method|0.5µl/5min x2 depths|
|&#x00A0;Tracer **4** |TET-smFP-myc (thy1-tTA 1/TRE-smFP-myc 1)x10e12 vg/ml|
|&#x00A0;Injection Site|AP=0, R=6.5|
|&#x00A0;Direction|antero|
|&#x00A0;Method|0.1 µl/5 min @ 0.7 mm|
|&#x00A0;Tracer **5** |TET-smFP-FLAG (thy1-tTA 1/TRE-smFP-FLAG 1)x10e12 vg/ml|
|&#x00A0;Injection Site|AP=0, R=4.3|
|&#x00A0;Direction|antero|
|&#x00A0;Method|0.1 µl/5 min @ 0.7 mm|
|&#x00A0;Tracer **6** |TET-smFP-HA (thy1-tTA 1/TRE-smFP-HA 1)x10e12 vg/ml|
|&#x00A0;Injection Site|AP=0, L=4.3|
|&#x00A0;Direction|antero|
|&#x00A0;Method|0.1 µl/5 min @ 0.7 mm|


## CONTENT

| File name | Description |
| ---- | ---- |
|[`NN_tracer`](NN_tracer)/||
|[`c2_50mu`](c2_50mu)/||
|[`labels`](labels)/||
|[`c1_50mu`](c1_50mu)/||
|[`c3_50mu`](c3_50mu)/||
|[`Backlit_slices`](Backlit_slices)/||
|[`Nissl_slices`](Nissl_slices)/||

**Note:** Color lookup table used in [atlas region labels slices](labels) can be found [here](https://cau-gin.brainminds.riken.jp/brainminds/BMA-2017/src/master/bma-1-clut.ctbl).
initial release 2021-12-27 00:00:00 +09:00			`# Marmoset Tracer-Injection [R01_0110]`

			`Authors: Akiya Watakabe<sup>1</sup>*, Henrik Skibbe<sup>2</sup>`

			`1. Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science`
			`2. Brain Image Analysis Unit, RIKEN Center for Brain Science`

			`*corresponding authors: Akiya Watakabe (akiya.watakabe@riken.jp)`


			`## DATASET DESCRIPTION`

			`This dataset contains TissueCyte images produced during tracer injection experiment on Marmoset R01_0110`

			`* Microscopy images and annotations: Akiya Watakabe.`
			`* Image post-processing: Henrik Skibbe.`


			`For more details see https://dataportal.brainminds.jp/marmoset-tracer-injection`


			`## EXPERIMENT METADATA`
			`\|\|\|`
			`\|----\|-----\|`
			`\|Brain/MINDS ID\|R01_0110\|`
			`\|Group\|Yamamori\|`
			`\|Lab identifier\|TT77\|`
			`\|Region of injection\|A45\|`
			`\|Side of injection\|left\|`
			`\|Summary\|A45 injection. Small spread in A47L. Weak tracer signals. Projections to visual areas may suggest its position as FEF for small saccade. \|`
			`\|Known issues\|Expression is low. In particular, low expession in layer 6. Potential interference of AAV-smFP constructs.\|`
			`\|Age\|6.7\|`
			`\|Sex\|F\|`
			`\|Body weight (g)\|386\|`
			`\|Date of birth\|20120719\|`
			`\|Injection date\|20190219\|`
			`\|Survival period (day)\|27\|`
			`\| Tracer 1 \|(thy1-tTA 1/TRE-clover 1/TRE-Vamp2mPFC 0.25)x10e12 vg/ml\|`
			`\| Direction\|anterograde\|`
			`\| Method\|0.2ul x 1 (@ 1.8 mm) 5min \|`
			`\| Tracer 2 \|AAV2retro-EF1-cre: 1.5x10e12 vg/ml\|`
			`\| Injection Site\|Coinjection with tracer 1\|`
			`\| Direction\|retro\|`
			`\| Tracer 3 \|10 % BDA\|`
			`\| Injection Site\|contra/MT\|`
			`\| Direction\|antero\|`
			`\| Method\|0.5µl/5min x2 depths\|`
			`\| Tracer 4 \|TET-smFP-myc (thy1-tTA 1/TRE-smFP-myc 1)x10e12 vg/ml\|`
			`\| Injection Site\|AP=0, R=6.5\|`
			`\| Direction\|antero\|`
			`\| Method\|0.1 µl/5 min @ 0.7 mm\|`
			`\| Tracer 5 \|TET-smFP-FLAG (thy1-tTA 1/TRE-smFP-FLAG 1)x10e12 vg/ml\|`
			`\| Injection Site\|AP=0, R=4.3\|`
			`\| Direction\|antero\|`
			`\| Method\|0.1 µl/5 min @ 0.7 mm\|`
			`\| Tracer 6 \|TET-smFP-HA (thy1-tTA 1/TRE-smFP-HA 1)x10e12 vg/ml\|`
			`\| Injection Site\|AP=0, L=4.3\|`
			`\| Direction\|antero\|`
			`\| Method\|0.1 µl/5 min @ 0.7 mm\|`


			`## CONTENT`

			`\| File name \| Description \|`
			`\| ---- \| ---- \|`
			\|[`NN_tracer`](NN_tracer)/\|\|
			\|[`c2_50mu`](c2_50mu)/\|\|
			\|[`labels`](labels)/\|\|
add c1, c3, backlit & nissl slices 2023-08-17 00:00:00 +09:00			\|[`c1_50mu`](c1_50mu)/\|\|
			\|[`c3_50mu`](c3_50mu)/\|\|
			\|[`Backlit_slices`](Backlit_slices)/\|\|
			\|[`Nissl_slices`](Nissl_slices)/\|\|
add link to region lookup table 2023-09-14 00:00:00 +09:00
			`Note: Color lookup table used in [atlas region labels slices](labels) can be found [here](https://cau-gin.brainminds.riken.jp/brainminds/BMA-2017/src/master/bma-1-clut.ctbl).`